This is an open access article published under a Creative Commons Attribution (CC-BY) License, which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited.
Article pubs.acs.org/jcim
Matched Peptides: Tuning Matched Molecular Pair Analysis for Biopharmaceutical Applications Julian E. Fuchs,*,† Bernd Wellenzohn,‡ Nils Weskamp,‡ and Klaus R. Liedl† †
Theoretical Chemistry, Faculty of Chemistry and Pharmacy, University of Innsbruck, Innrain 82, 6020 Innsbruck, Austria Research Germany/Lead Identification and Optimization Support, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach an der Riss, Germany
‡
S Supporting Information *
ABSTRACT: Biopharmaceuticals hold great promise for the future of drug discovery. Nevertheless, rational drug design strategies are mainly focused on the discovery of small synthetic molecules. Herein we present matched peptides, an innovative analysis technique for biological data related to peptide and protein sequences. It represents an extension of matched molecular pair analysis toward macromolecular sequence data and allows quantitative predictions of the effect of single amino acid substitutions on the basis of statistical data on known transformations. We demonstrate the application of matched peptides to a data set of major histocompatibility complex class II peptide ligands and discuss the trends captured with respect to classical quantitative structure−activity relationship approaches as well as structural aspects of the investigated protein−peptide interface. We expect our novel readily interpretable tool at the interface of cheminformatics and bioinformatics to support the rational design of biopharmaceuticals and give directions for further development of the presented methodology.
■
comparative modeling techniques have been described.17 These 3D techniques have to cover the bioactive conformation of the usually highly flexible peptide ligands, which poses additional challenges for modeling.18 In a pioneering study, Sneath derived the first molecular descriptors for the 20 natural amino acids and applied them in QSAR modeling.19 Later, these 2D descriptors were refined to capture chemically intuitive information via the Z-scale model20 or the isotropic surface area/electronic charge index (ISA/ECI) model.21 In contrast to substitution matrices frequently applied in bioinformatics (e.g., PAM,22 BLOSUM23), these descriptors are designed to reflect chemical in contrast to evolutionary similarity. Amino acid descriptors have typically been used to derive QSAR equations by linear regression techniques.24 Over the past decade, the innovative cheminformatic concept of “matched molecular pair analysis”25 has been gaining increasing attention. Herein, pairs of molecules with a single difference in chemical structure are analyzed with respect to changes in a physicochemical or biological property.26 Data mining in large databases (e.g., bioactivities stored in ChEMBL27 or in-house data sets28) allows trends from matched molecular pairs or matched molecular series to be applied subsequently for prediction of substitution effects in new molecules.29 A key advantage of matched molecular pair analysis is the direct chemical interpretability of predictions (“white box”) based on local SAR rules.30 Recently, efforts have
INTRODUCTION Biopharmaceuticals are defined as pharmaceutical products consisting of (glyco)proteins and/or nucleic acids.1 Therefore, this class of drugs mainly comprises peptide hormones, recombinant proteins, monoclonal antibodies, and therapeutic antibodies. Biopharmaceuticals allow access to new target classes and are therefore considered more innovative than small-molecule drugs.2 Accordingly, a record number of 11 new biopharmaceuticals were approved by the FDA in 2014.3 Therefore, biopharmaceuticals hold promise to claim a larger share of the drug market in the future.4 Additionally, biosimilars are increasingly entering the market after patent expiry of original biopharmaceutical products.5 Biopharmaceuticals generally pose new challenges for the drug discovery process, which has historically been focused on small molecules. This includes their analytical characterization,6 delivery and formulation7,8 after optimization of the biotechnological production process,9,10 and their molecular properties.11 Computational modeling techniques hold great promise to handle the complexity of the generated data and, for example, to guide affinity optimization of therapeutic proteins12 or peptides.13,14 Peptide drugs are often considered as the border between small-molecule drugs and biopharmaceuticals, as their synthesis is mainly chemistry-driven.15 Traditionally, quantitative structure−activity relationship (QSAR) and quantitative structure−property relationship (QSPR) modeling approaches neglect the three-dimensional (3D) structure of the peptides and proteins and are thus 2Dbased. Nevertheless, approaches using 3D interaction fields16 or © XXXX American Chemical Society
Received: July 31, 2015
A
DOI: 10.1021/acs.jcim.5b00476 J. Chem. Inf. Model. XXXX, XXX, XXX−XXX
Article
Journal of Chemical Information and Modeling
Figure 1. Matched molecular pairs and matched peptides. The correspondence of matched molecular pairs to matched peptides is exemplified by the chemical transformation of benzene to toluene by exchange of a hydrogen for a methyl group (orange). The same transformation is involved when an alanine-glycine-alanine tripeptide is exchanged with alanine-alanine-alanine. The latter transformation may be easily encoded when using standard one-letter amino acid codes. This representation allows for fast processing of large databases connecting sequences with respective molecular properties.
peptides. For identification of these single substitutions, a pairwise sequence alignment that can be performed by standard bioinformatics methodologies is required. Sequence alignment for matched peptides is trivial since they consistently differ by a single amino acid. This sequence alignment step simplifies the graph matching problem for small molecules described above, since linear peptides have the advantage of having defined Cand N-termini as well as identical chemical backbones (see Figure 1). Furthermore, insertions and deletions between sequence pairs can be considered as trivial additions to the exchange of single amino acids and thus may also be involved as additional transformations in matched peptides. Matched peptides therefore represent a special case of matched molecular pairs that are easy to detect on the sequence level. Code implementation was performed using standard Python tools in combination with a custom node in KNIME44 aiming to identify all sequence pairs differing in a single sequence position and thus forming matched peptide pairs. Since all of the sequences analyzed in the current study were point mutations relative to a consensus sequence and had a constant length, no gaps occurred, and the presented analysis is therefore independent of gap penalties in the alignment step. Affinity differences observed for matched peptides were aggregated over all peptide positions, assuming that the effects of amino acid exchanges are independent of their position and thus reflect an average of all binding-site environments. We will demonstrate in the Results and Discussion section that this assumption is in general valid for MHC II binders and also discuss ways to cover position-specific aspects in matched peptide analysis. Analyzed Data Set. We analyzed experimental binding affinities for a panel of 198 peptides toward MHC II molecules from Marshall et al.45 Fluorescence-based assays were applied to obtain IC50 values in the nano- and subnanomolar range for all of the peptides using a 12-point inhibition curve for binding with three replicates each. Peptide sequence were grouped around the template peptide sequence AAYAAAAAAAAAA, where the central 11 amino acids of the peptide with length 13 were varied. For positions 2 and 4 to 12, all 20 natural amino acids were tested, while only seven apolar amino acids (F, I, L,
been made to put purely ligand-based matched molecular pairs into structural context and thereby identify the structural background of observed bioactivity trends.31,32 Herein we expand the scope of matched molecular pairs to the analysis of macromolecular data from proteins and peptides and introduce matched peptides, a concept we expect to hold great promise for the development of biopharmaceuticals. As an example application, we investigate peptide binding to the major histocompatibility complex class II (MHC II), a surface receptor crucial for T-cell activation in immune response.33,34 A crystal structure of the receptor shows that the peptide is bound to a hydrophobic surface groove that is flanked by two αhelices.35 Through the availability of structural information, most modeling approaches aiming at the prediction of peptide binding to MHC molecules employ machine learning techniques,36 e.g., MULTIPRED.37 Large peptide data sets have been compiled and used for the optimization of consensus approaches based on machine learning methods.38 Application of these techniques allows for the optimization of peptides with desired immunological properties.39 Quantitative modeling techniques are rarely applied toward MHC binding but include classical amino acid-descriptor-based QSAR methods40 as well as molecular dynamics simulation approaches.41 Here we apply the novel matched peptides strategy to the prediction of MHC II binding affinities and demonstrate the direct interpretability of the predictions in a structural context.
■
METHODS Matched Molecular Pairs and Matched Peptides. Identification of matched molecular pairs involves an exhaustive pairwise matching of molecular graphs. To simplify this task, molecules are usually fragmented to aid the search for corresponding substructures.42 Older implementations additionally required a definition of the allowed transformations within matched pairs,43 thus prohibiting the identification of unknown chemical modifications associated with a change in the molecular property under investigation. In the context of peptide and protein data, a molecular transformation corresponds to a point mutation. Therefore, sequences differing by a single character correspond to matched B
DOI: 10.1021/acs.jcim.5b00476 J. Chem. Inf. Model. XXXX, XXX, XXX−XXX
Article
Journal of Chemical Information and Modeling
we extracted trends on how amino acid substitutions increase and decrease molecular interactions via matched peptide analysis. In total we extracted 2117 matched peptides that formed the basis of the statistical evaluation. The order of identified matched pairs was normalized to consistently reflect gains in affinity. The amino acid substitutions with the strongest effects on the observed binding affinities are summarized in Table 1.
M, V, W, Y) were tested for position 3. All of the sequences represent single-point mutations around the template sequence. Additionally, the length of the peptide (13 amino acids) was kept constant, and thus, no insertions or deletions were present among the matched peptide sequences. All of the presented analyses are based on negative decadic logarithms of reported IC50 values and their ratios based on molar units. Statistical Framework. On the basis of statistical analysis of bioactivity data from ChEMBL, the expected standard deviation of the IC50 data from a homogeneous source is 0.2 log units.46 Therefore, an average effect size of at least 0.20 log units establishes statistical significance versus the null hypothesis (no change in activity) at the p = 0.05 level with at least 10 matched molecular pairs or matched peptides.47 Therefore, the term “significant transformations” used later on explicitly refers to those amino acid substitutions associated with an effect on the binding affinity that is statistically significantly different to zero. Correlation to Amino Acid Descriptors. We correlated trends in bioactivities (affinity shifts) observed from analysis of matched peptides to differences in amino acid properties. Therefore, we employed three descriptors from the Z-scale approach describing hydrophilicity (z1), steric bulk (z2), and electronic properties (z3 ).20 Furthermore, we analyzed correlations to differences in the isotropic surface area (ISA) and the electronic charge index (ECI).21 Correlations between activity differences and property differences were assessed via calculation of Pearson’s linear correlation coefficient r and Spearman’s rank correlation coefficient ρ to capture both quantitative and qualitative dependences. Statistical analyses were performed using R.48 Structural Interpretation and Correlation to Peptide Specificity. To interpret the bioactivity data in structural context, we compared the observed trends to a cocrystal structure of an MHC II in complex with an antigenic peptide (PDB entry 1AQD49). We visualized the structure in Pymol50 and extracted polar contacts as well as electrostatic properties of the binding-site region using default settings. The specificities of respective MHC II binding-site regions were assessed on the basis of binding affinity distributions for single amino acids. Therefore, we converted the affinity ratios to decadic log units and analyzed the distribution of binding affinities for each single site. In the case of a highly specific region, major differences in binding affinity are expected, corresponding to a narrow peak in the distribution. On the contrary, a completely nonspecific position shows an equal distribution of binding affinities. Such experimental distributions can be converted to single values depicting local specificity via an information-entropy-based approach, as demonstrated earlier for amino acid distributions in protease substrates.51 Thereby, an entropy of 0 corresponds to the highest specificity, whereas a value of 1 corresponds to maximum binding promiscuity with constant binding affinities. All of the peptide residues except for position 3, where only seven of the 20 amino acids were tested, were examined individually.
Table 1. Transformations with Major Effects on the MHC II Binding Affinitya transformation
pairs
mean affinity difference [log units]
SEM [log units]
P→C P→Y P→L P→M D→C P→S P→N P→V P→A K→C
10 10 10 10 10 10 10 10 19 11
0.715 0.672 0.624 0.620 0.606 0.606 0.596 0.594 0.587 0.585
0.291 0.329 0.354 0.320 0.147 0.332 0.366 0.339 0.215 0.250
a
Matched peptides were used to extract the 10 substitutions leading to the largest changes in affinity. These transformations were normalized to reflect affinity increases and sorted according to decreasing effect size; the standard error of the mean (SEM) is indicated as measure of statistical uncertainty. Removal of proline residues increases the binding strength to MHC II molecules, as does the removal of charged residues. On the contrary, inclusion of cysteine residues increases the binding affinity to the receptor.
Overall, for 88 of 190 transformations (44%) we observed a significant change in binding affinity. The strongest effect was achieved by a replacement of proline by cysteine, leading to a gain of 0.715 log units, which corresponds to 5 times stronger binding. The standard error of the mean (SEM) observed over 10 examples for this transformation was 0.291 log units, which is much smaller than the average effect size. This indicates that replacement of proline by cysteine indeed leads to an increase in binding affinity largely independent of the peptide position where the transition occurs. Several additional substitutions of proline among the transformations with the strongest effects on binding affinity indicates that this residue is in general detrimental to MHC II binding. Replacement by smaller residues is favored, and especially the inclusion of cysteine residues leads to major gains in binding affinity. Additionally, replacement of charged residues is associated with gains in binding affinity. Within the top 10 transformations we found the substitution of aspartate and lysine by cysteine, both of which led to an affinity gain of approximately 0.6 log units, corresponding to a factor of 4 on a linear scale. The aspartate to cysteine transformation is associated with a particularly small SEM of 0.147, indicating particularly conserved effects over the whole binding-site region. In addition to 88 transformations with significant effects on the binding strength, we characterized 102 transformations associated with only minor changes in MHC II binding. Here we observed the absence of amino acids described to be associated with particularly weak or strong binding. Therefore, the frequency of cysteine residues and charged residues within these transformations was reduced or those residues were completely missing. We found several transformations involving
■
RESULTS AND DISCUSSION Trends in Binding Affinity from Matched Peptide Analysis. Applying matched peptides, we extracted information on quantitative changes in MHC II binding affinity induced by single-point mutations. On the basis of 198 peptide sequences and their respective experimental binding affinities, C
DOI: 10.1021/acs.jcim.5b00476 J. Chem. Inf. Model. XXXX, XXX, XXX−XXX
Article
Journal of Chemical Information and Modeling
binding peptides. Since the peptide transformations have been arranged to reflect gains in binding affinity, we counted the occurrence of all 20 amino acids on the left side of the transformation (Nleft, smaller activity) and on the right side (Nright, higher activity) among all 88 pairs showing a significant change in binding affinity. The differences in these occurrences (Nright − Nleft), which are given in Figure 2A, enable qualitative identification of favorable and unfavorable amino acids. We found six amino acids to be mainly disfavored in MHC II binding proteins: proline, all four charged amino acids (aspartate, glutamate, lysine, and arginine), and the polar amino acid glutamine. Glutamine shows a smaller negative effect (a total of five pairs with decreased affinity) than the other five amino acids, all of which exhibit very similar disruptive effects (a total of 14 or 15 pairs with decreased affinity). On the other end of the amino acid ranking, tyrosine was found to enhance the MHC II binding affinity in a total of nine significant peptide pairs, followed by cysteine, which was identified as a favorable replacement in a total of eight cases. Mostly small amino acids follow in the ranking, including alanine, methionine, asparagine, and serine. The difference in size might also explain the marked difference observed in comparisons of peptides containing asparagine versus glutamine. The smaller asparagine appears to be favorable for MHC II binding (+6 pairs), whereas glutamine is unfavorable (−5 pairs). Quantitative Effects of Amino Acid Exchanges. A similar analysis can be performed on the basis of the average effect size rather than the occurrence of amino acids on each side of the transformation. Here, all of the transformations, including those with insignificant effects on the binding affinity, were analyzed to yield a quantitative ranking of amino acid contributions to MHC II binding affinities (see Figure 2B). Consistent with the other presented analyses, proline is associated with a major decrease in MHC II binding affinity representing the strongest effect observed within the data set. On average, 0.474 log units can be gained by replacement of a proline with any other natural amino acid. A replacement of either charged amino acid leads to a gain of between 0.31 and 0.36 log units, thus halving the binding affinity. On the other end of the spectrum, the introduction of cysteine and tyrosine residues is favored and leads to a gain in affinity by 0.26 to 0.28 log unit. Several mainly small and hydrophobic residues are
small amino acids that appear to be readily interchangeable within MHC II binding peptides (see Table 2). This behavior is Table 2. Transformations with Little Effect on Binding Affinitya transformation
pairs
V→I T→H V→N I→W L→F V→W G→T A→V G→H N→S
11 10 10 11 11 11 10 19 10 10
mean affinity difference [log units] SEM [log units]
